REPLICATION DATA FOR: Auditing the Human BioMolecular Atlas Program (HuBMAP) Human Reference Atlas (HRA): An Evaluation of Core Digital Objects

Authors: Devan Ray Donaldson, Mary Nelson, Katy Börner
Affiliation: Indiana University Luddy School of Informatics, Computing, and Engineering
Contact: drdonald@iu.edu
Date: 2026


DESCRIPTION
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This dataset contains the audit instruments and evaluation results from the first independent third-party audit of the Human Reference Atlas (HRA), produced by the Human BioMolecular Atlas Program (HuBMAP). The audit was conducted iteratively between March 2024 and August 2025 using publicly accessible data from HRA v2.1 (7th release).


FILE DESCRIPTIONS
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1. asctb_metadata_audit_rows1-10.csv
   Row-by-row metadata compliance evaluation of Rows 1-10 across 34 ASCT+B tables.
   Evaluates conformance to SOP requirements: organ names, author information, 
   ontology identifiers, reviewer details, and FTU DOIs. Contains PURLs linking 
   to version-specific ASCT+B tables (e.g., https://purl.humanatlas.io/asct-b/thymus/v1.4).

2. 2d_ftu_style_guide_audit.csv
   Assessment of 22 2D Functional Tissue Unit illustrations across 10 organs.
   Evaluation criteria derived from Bajema (2022) style guide including: palette 
   differentiation of anatomical structures and cell types, dark gray outlines, 
   leader line formatting, leader line angles (45° or 90°, conditional per style 
   guide), high contrast rendering, scale bars, and HRA icons.

3. 3d_reference_objects_audit.csv
   Evaluation of 30 3D Reference Objects for functional usability including:
   presence of male/female variants, left/right laterality where applicable, 
   and interactive rotation capability.

4. omap_required_fields_audit.csv
   Completeness audit of 21 Organ Mapping Antibody Panels (OMAPs) against 
   13 evaluated criteria (9 required, 4 optional) specified in or derived from 
   Radtke et al. (2022) SOP. Required fields include: Anatomical Structures, 
   Cell Types, Protein Biomarkers, imaging modality, tissue preservation method, 
   protocol links, discussion of missing cell types, FFPE antigen retrieval 
   method, and antibody placement notes. Optional fields include: discussion of 
   other OMAPs/studies, specific application highlights, analytical pipeline 
   details, and custom conjugation/detection methods.

5. asctb_structural_integrity_formulas.xlsx
   Excel formulas used to evaluate hierarchical contiguity and structural 
   integrity of ASCT+B tables. Formulas implement nested logical checks 
   (IF, OR, AND, COUNTA) to detect non-contiguous pathways in Anatomical 
   Structure, Cell Type, and Biomarker columns. 
   
   Preserved as XLSX to retain formula logic as methodology documentation.
   
   Usage: Copy formulas to corresponding columns in an ASCT+B table. Formulas 
   return TRUE for valid rows with contiguous hierarchies; FALSE indicates 
   structural discontinuities (e.g., AS/3 blank while AS/4 is populated).
   Formulas include ROW()<11 condition to exclude metadata rows 1-10.

6. asctb_presence_formatting_audit.csv
   Row-level presence and formatting compliance evaluation across all 34 
   ASCT+B tables. Evaluates whether required fields contain data (presence) 
   and whether populated fields conform to SOP formatting specifications 
   (formatting compliance). Source data for the 95.89% average presence and 
   79.12% average formatting compliance rates reported in the paper.


METHODOLOGY
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Audit criteria were derived from published HuBMAP Standard Operating Procedures and Style Guides:

- ASCT+B tables: 
  Quardokus, E. M., Record, E., & Herr, B. W., II. (2022). SOP: Authoring 
  Anatomical Structures, Cell Types and Biomarkers (ASCT+B) tables (v2.1.0). 
  Zenodo. https://doi.org/10.5281/zenodo.7382751

- 2D FTU illustrations: 
  Bajema, R. (2022). Style guide: Human Reference Atlas 2D Functional Tissue 
  Unit (FTU) illustrations (v4.0.0). Zenodo. 
  https://doi.org/10.5281/zenodo.6703377

- 3D Reference Objects:
  Quardokus, E. M., Bueckle, A., Börner, K., Record, E., & Browne, K. (2022). 
  SOP: 3D Reference Object Approval (v2.2.0). Zenodo. 
  https://doi.org/10.5281/zenodo.5944197
  Note: This process-oriented SOP emphasizes workflow and iterative SME review 
  rather than checklist-based criteria, so evaluation focused on functional 
  usability rather than independent anatomical verification.

- OMAPs: 
  Radtke, A. J., Quardokus, E. M., & Saunders, D. C. (2022). SOP: Construction 
  of organ mapping antibody panels for multiplexed antibody-based imaging of 
  human tissues (v2.0.0). Zenodo. https://doi.org/10.5281/zenodo.7386417

The audit methodology combines four components:
1. SOP-to-checklist operationalization
2. Formula-based consistency checks
3. Tiered compliance assessment (quantitative for structured data, qualitative 
   for visual objects)
4. Iterative feedback loops with HuBMAP curatorial team


DATA ACCESS NOTES
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The ASCT+B tables evaluated in this audit are NOT redistributed in this dataset. 
They are accessible via version-specific Persistent URLs (PURLs) documented in 
asctb_metadata_audit_rows1-10.csv.

Example PURL: https://purl.humanatlas.io/asct-b/thymus/v1.4

These PURLs resolve to the specific table versions audited (HRA v2.1, 7th release). 
For current versions, visit the HRA Portal: https://humanatlas.io/asctb-tables

All original HuBMAP/HRA data is available under Creative Commons Attribution 4.0 
International License (CC BY 4.0) from the Human Reference Atlas Portal.


VERSION NOTES
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- Data audited: HRA v2.1 (7th release), accessed via HuBMAP Data Portal
- Audit period: March 2024 - August 2025
- Issues identified in this audit were subsequently addressed in HRA v2.3
- Structural contiguity violations were documented in 3 of 34 ASCT+B tables:
  Kidney (2 rows), Thymus (7 rows), and Ureter (1 row)
- Biomarker depth incompleteness (non-structural) was documented in 3 additional 
  organs: Kidney (5 rows), Large Intestine (11 rows), and Liver (1 row)


SUMMARY OF FINDINGS
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Overall compliance rate across all four digital object types: 94.7%

Compliance rates by digital object type:
- ASCT+B tables: 88.67% composite (95.89% metadata presence, 79.12% formatting 
  compliance, 91% structural contiguity)
- 2D FTU illustrations: 92.50% average style guide conformance across 8 criteria
  (range: 59.1-100%)
- 3D Reference Objects: 100% functional usability
- OMAPs: 97.8% average compliance across 13 evaluated criteria (96.8% for 
  9 required fields only; range: 76.2-100%)

Structural contiguity violations were identified in 3 of 34 ASCT+B tables (8.8%):
- Kidney: 2 rows with missing AS/4 values producing non-contiguous pathways
- Thymus: 7 rows with missing AS/4-AS/5 values producing non-contiguous pathways
- Ureter: 1 row with missing AS/2 value producing non-contiguous pathway

Biomarker depth incompleteness (non-structural) was identified in 3 organs:
- Kidney: 5 rows with missing BGene values at intermediate levels
- Large Intestine: 11 rows with missing BGene/5 and BProtein/5 values
- Liver: 1 row with missing BProtein/2 value


FUNDING
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This research was supported by the National Institutes of Health (NIH) Office 
of the Director through an Other Transaction award (Award Number OT2OD033756, 
"3D Multiscale Biomolecular Human Reference Atlas Construction, Visualization 
and Usage").


ETHICS STATEMENT
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This project was reviewed by Indiana University's Human Subjects Office and 
determined not to constitute human subjects research.


RELATED PUBLICATION
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Donaldson, D. R., Nelson, M., & Börner, K. (2026). Auditing the Human 
BioMolecular Atlas Program (HuBMAP) Human Reference Atlas (HRA): An Evaluation 
of Core Digital Objects. International Journal of Digital Curation. 
[DOI to be added upon publication]


LICENSE
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This dataset is released under Creative Commons Attribution 4.0 International 
License (CC BY 4.0).

When using this dataset, please cite both this dataset and the associated 
publication.
